Protein Model and Function Analysis in Quorum-Sensing Pathway of Vibrio qinghaiensis sp.-Q67

Simple Summary Vibrio qinghaiensis sp.-Q67 (Q67) is a nonpathogenic freshwater luminescent bacterium and has been a focus due to its wide use in the monitoring of environmental pollution and the assessment of toxicity, using the luminescence inhibition rate as the end point. However, the lack of available crystal structures limits the elucidation of the structures of the functional proteins of the quorum-sensing (QS) system that regulates bacterial luminescence in Q67. In this study, homologous models of 19 proteins potentially involved in QS and bioluminescence in Q67 were built using MODELLER. Then, we analyzed the predicted structures and functions of these proteins one by one by combining the existing proteins to explore how the QS pathway of Q67 regulated bioluminescence at the molecular level. This study not only provides a database of predicted protein molecular structures for exploring the mechanisms of the toxicity of chemicals from a molecular point of view, but also indirectly summarizes the research status of crystal structure and function analysis in QS systems, providing references and guidance for follow-up research. Abstract Bioluminescent bacteria are mainly found in marine habitats. Vibrio qinghaiensis sp.-Q67 (Q67), a nonpathogenic freshwater bacterium, has been a focus due to its wide use in the monitoring of environmental pollution and the assessment of toxicity. However, the lack of available crystal structures limits the elucidation of the structures of the functional proteins of the quorum-sensing (QS) system that regulates bacterial luminescence in Q67. In this study, 19 functional proteins were built through monomer and oligomer modeling based on their coding proteins in the QS system of Q67 using MODELLER. Except for the failure to construct LuxM due to the lack of a suitable template, 18 functional proteins were successfully constructed. Furthermore, the relationships between the function and predicted structures of 19 functional proteins were explored one by one according to the three functional classifications: autoinducer synthases and receptors, signal transmission proteins (phosphotransferases, an RNA chaperone, and a transcriptional regulator), and enzymes involved in bacterial bioluminescence reactions. This is the first analysis of the whole process of bioluminescence regulation from the perspective of nonpathogenic freshwater bacteria at the molecular level. It provides a theoretical basis for the explanation of applications of Q67 in which luminescent inhibition is used as the endpoint.